The final book in the Shadow Academy series explodes in the reader's hands with non-stop action and the final confrontation between good and evil. The story begins with an Imperial scout trooper disabling the shield generator of the Jedi Academy, leaving Yavin 4 open for a swift attack. Now fully trained Jedi with their own lightsabers, the young Jedi Knights quickly work together to stop the incoming threat. After Luke briefs all of his students for the battle to come, the twins disband to try and fix the generator and to call for help.

While Jacen and Zekk's good friend Peckhum blast into space to send out a call for help, they are chased by TIE fighters flown by Zekk's former friends. After sending out a distress signal, Jacen and Peckhum dive back into the atmosphere of Yavin 4, about to be obliterated by TIEs. But they are saved at the last second by a familiar face... Qorl, the imperial pilot. Meanwhile Lowie and Tenel Ka attack the landing platform that is unloading Dark Jedi into the jungles of Yavin 4. Eventually Tenel Ka tracks down her nemesis, Tamith Kai, and engages her in a fierce lightsaber battle. Soon after the platform explodes, and while Lowie and Tenel Ka escape, Tamith Kai does not.

Jaina, on a mission to repair the shield generator, is confronted by her former friend turned Dark Jedi Knight Zekk, who is assigned to destroy what's left of the Jedi. In the end, Zekk saves the Jedi by stopping them from returning to the Academy, which is destroyed by a bomb placed in the main audience chamber. Luke tries his best to turn his former student Brakiss back to the light side, just before they engage in an epic lightsaber duel. Luke is soon victorious, and Brakiss flees back to the Shadow Academy. But as the Jedi's re-enforcements arrive—in the form of Lando Calrissian and his GemDiver Station—the Emperor's guardsmen, who have been faking the Emperor's existence from the start of the series, reveal the face of the Emperor. The Emperor panics and engages the Shadow Academy's self-destruct. The Dark Jedi's base is instantly destroyed, with Brakiss on it. By the end of the story, all of the Jedi are battered, bruised, and barely alive. But the Dark Side has lost, Zekk has become the boy they once knew, and the Academy can be rebuilt. It is a day of victory.